Blender save files wrong
Blender saves the files correctly.
Ngons have nothing to do with this (always search for the meaning of words before using them).
Different applications support different formats of 3d objects and object attributes. No single application is compatible with the many different formats that exist.
To open the files in a different app, then you have to export in a format that the other app can deal with.
When you convert an object to another format, not all attributes (textures, animations, constraints, modifiers, armatures or simulations) will be saved a s part of a format that does not support such attributes.